Madara is a known liar. He is supposed to be a confusing character. That's why ditching the Madara = Danzou theory without solid evidence is foolish. It is still logically consistent that Danzou is Madara. Or not. The story hasn't told us enough to decide one way or the other.

Here are some things that are "known" about Madara:

(1) Madara gains the MS, and establishes the Uchiha training method of killing your friend for it.
(2) Madara takes his brother's eyes to gain the EMS.
(3) Madara and Hashirama fight for Konoha.
(4) At some point between (3) and (5), Madara becomes Mizukage and institutes the Uchiha training method. That much is (more-or-less) known to be true.
(5) 100 years later, Madara attacks Konoha with the Kyuubi.
(6) Madara and Itachi kill the Uchiha, on Danzou's order (though Madara just did it for the fun of it, supposedly)
(7) Tobi joins Akatsuki, captures Sanbi, helps Deidara fight Sasuke (a little).
(8) Madara reveals himself to a few people, and starts giving Pein orders, eventually orders Pein to capture Naruto.
(9) Madara almost eats an Amaterasu from Sasuke, sent by Itachi.
(10) Madara tells parts of this story (but crucially, lies about (5) and potentially others) to Sasuke.
(11) Tells Sasuke that Pein destroyed Konoha, had intended to use Rinne Tensei for his own purposes.

(6) is probably the most interesting, for the Danzou is Madara theory. How could Madara have known about the mission and shown himself to Itachi, if Madara isn't connected to Danzou somehow? This was such a top secret mission that only Danzou, Sandaime Hokage, the Advisors, and Itachi knew about it. In fact, considering that Danzou ordered it, it might have even been a Roots mission. In this part of the story, Madara says that Itachi seeked him out.

(1) is also interesting, since Roots uses the same training methods that the Uchiha and the Land of Mist used.

Here's a summary of things "known" about Danzou:

(A) Origins unknown, age approximately 70-80, fought Sandaime Hokage for the title. Hawkish diplomacy incompatible with Senju's Will of Fire.
(B) Founded his own ANBU, called Roots, which used the Uchiha training method
(C) Joins Hanzo in destroying "proto-Akatsuki", is among the first people in the world to see Gedo Mazo.
(D) Ordered the extermination of the Uchiha (which Madara was more than happy to help with!)
(E) Itachi threatens Danzou, in order to protect Sasuke. This is told to us by Madara.
(F) Sent Sai "to kill" Sasuke
(G) Killed the messenger frog to keep Naruto out of the village
(H) Doesn't help in the fight against Pein.
(I) Has a hurt arm and a Sharingan.

(C) is an interesting connection between Danzou and Nagato, since Nagato revealed the weapon that Madara now wants to Danzou and Hanzo. (D) speaks for itself. (E) Speaks for itself. This "should" have been ultra-top secret, but for some reason Madara knows all about it. (I) Speaks for itself. Danzou has a hurt arm and a Sharingan... So does Madara. http://www.onemanga.com/Naruto/397/03/